Hardcore PubMeding (advanced PubMed searching) - Revision history

Lee Farrand at 11:52, 22 January 2009

2009-01-22T11:52:07Z

←Older revision		Revision as of 11:52, 22 January 2009
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	'''PubMed''' [http://en.wikipedia.org/wiki/PubMed] at http://www.pubmed.org is maybe the '''best search machine for articles in biology'''. It is run by the NCBI [http://www.ncbi.nlm.nih.gov/], USA, and gives you the possibility to search a gigantic archive of life science literature.		'''PubMed''' [http://en.wikipedia.org/wiki/PubMed] at http://www.pubmed.org is maybe the '''best search machine for articles in biology'''. It is run by the NCBI [http://www.ncbi.nlm.nih.gov/], USA, and gives you the possibility to search a gigantic archive of life science literature.

-	But searching is not easy. Type almost any single term and you will get thousands of hits which you will never be able to browse let alone read. So, to find your preferred needle in the haystack you will need to learn how wring the best out of PubMed.	+	But searching is not easy. Type almost any single term and you will get thousands of hits which you will never be able to browse let alone read. So, to find your preferred needle in the haystack you will need to learn how to wring the best out of PubMed.

	Below you find some tips how to become a hardcore PubMeder. Please add your own tricks if you miss them on this page.		Below you find some tips how to become a hardcore PubMeder. Please add your own tricks if you miss them on this page.

Barry Canton: /* Automatic search string interpretation */

2007-06-16T23:16:15Z

Automatic search string interpretation

←Older revision		Revision as of 23:16, 16 June 2007
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	=== Automatic search string interpretation ===		=== Automatic search string interpretation ===
-	PubMed doesn't just search 1:1 for what you type. Instead it ~~processed~~ your search string and tries to return the best results. Usually, this helps, esp. if you are not using field identifiers as described above. However, sometimes in can create problems. Try searching for the author "Black" without field names by just typing ''Black'' into the search box. Search and then click the '''Details tab'''. This tells you how PubMed interpreted your search string. You will see the following:	+	PubMed doesn't just search 1:1 for what you type. Instead it processes your search string and tries to return the best results. Usually, this helps, esp. if you are not using field identifiers as described above. However, sometimes in can create problems. Try searching for the author "Black" without field names by just typing ''Black'' into the search box. Search and then click the '''Details tab'''. This tells you how PubMed interpreted your search string. You will see the following:

	<pre>		<pre>

Jakob Suckale: /* Problems */ copy and paste to PubMed

2007-06-16T10:32:45Z

Problems: copy and paste to PubMed

←Older revision		Revision as of 10:32, 16 June 2007
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	Not exactly what you wanted probably. Black is a synonym for the MeSH term ''African American''. It actually doesn't return any hits for Black as an author. You can remedy the situation either by giving initials ''Black S'' or by appending the [au] field name.		Not exactly what you wanted probably. Black is a synonym for the MeSH term ''African American''. It actually doesn't return any hits for Black as an author. You can remedy the situation either by giving initials ''Black S'' or by appending the [au] field name.
		+
		+	=== Copying and pasting to PubMed ===
		+	You just spotted an interesting paper in the reference list of a paper. So, you set about to copy and paste that reference to PubMed to read the abstract and copy it into your reference manager.
		+
		+	This method often doesn't work because PubMed is quite picky about formating. The easy solution is to use ''Google Scholar'' instead which is much more flexible. From there you can go back to PubMed if you need the PMID for example.
		+
		+	To illustrate the problem, here are 2 examples:
		+	# try searching for "''Venter C. et al. Science''" - no results since PubMed chokes on the ''et al.''; if you copy from journals that abbreviate their author lists using "et al."; again the '''Details''' tab is your best friend to find out why this didn't work: "Venter C.[Author] AND '''et al.[Author]''' AND ("science"[MeSH Terms] OR Science[Text Word])"
		+	# try "''Laemmli, U.K. T4''" - 1 result, but not from Laemmli; the '''Details''' show: "Laemmli[All Fields] AND U.K.[All Fields] AND T4[All Fields]"; Here the comma is the main problem due to which initials and last names are not recognised as belonging together. Remove it and you'll get the right results. Punctuation is generally a bad idea when searching PubMed. It's usually best just to remove any.

	== Further reading ==		== Further reading ==

Jakob Suckale: problem section

2007-06-15T16:33:23Z

problem section

←Older revision		Revision as of 16:33, 15 June 2007
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	PubMed includes a very useful function to suggest related articles to the one(s) you just retrieved by a search. The feature relates articles by comparing their words [http://www.ncbi.nlm.nih.gov/entrez/query/static/computation.html]. You will find them on the right of the abstract page. Often this will help you to find article not spotted by your search but of interest to you.		PubMed includes a very useful function to suggest related articles to the one(s) you just retrieved by a search. The feature relates articles by comparing their words [http://www.ncbi.nlm.nih.gov/entrez/query/static/computation.html]. You will find them on the right of the abstract page. Often this will help you to find article not spotted by your search but of interest to you.
		+
		+	== Problems ==
		+
		+	=== Automatic search string interpretation ===
		+	PubMed doesn't just search 1:1 for what you type. Instead it processed your search string and tries to return the best results. Usually, this helps, esp. if you are not using field identifiers as described above. However, sometimes in can create problems. Try searching for the author "Black" without field names by just typing ''Black'' into the search box. Search and then click the '''Details tab'''. This tells you how PubMed interpreted your search string. You will see the following:
		+
		+	<pre>
		+	"african continental ancestry group"[MeSH Terms] OR
		+	("african americans"[TIAB] NOT Medline[SB]) OR
		+	"african americans"[MeSH Terms]
		+	OR Black[Text Word]
		+	</pre>
		+
		+	Not exactly what you wanted probably. Black is a synonym for the MeSH term ''African American''. It actually doesn't return any hits for Black as an author. You can remedy the situation either by giving initials ''Black S'' or by appending the [au] field name.

	== Further reading ==		== Further reading ==

Jakob Suckale: /* MeSH - standardised keywords */ "Details tab" comment

2007-06-06T10:41:05Z

MeSH - standardised keywords: "Details tab" comment

←Older revision		Revision as of 10:41, 6 June 2007
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	See this [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Search_Field_Descrip PubMed help page] for a complete list.		See this [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Search_Field_Descrip PubMed help page] for a complete list.
		+
		+	PubMed is trying hard to guess what you were really looking for. To find out how the search engine interpreted what you typed, click on the "Details" tab after the search has been run.

	== My NCBI - personalising PubMed ==		== My NCBI - personalising PubMed ==

Jakob Suckale: /* MeSH - standardised keywords */ table layout, [au] details

2007-06-06T10:38:05Z

MeSH - standardised keywords: table layout, [au] details

←Older revision		Revision as of 10:38, 6 June 2007
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	The NCBI provides you with standardised search vocabulary. This is advantageous because the right MeSH term (medical subject heading) will find all articles using various synonyms of the term. For example, a brute text search for ''translation'' will not return publications using the synonym ''protein synthesis''. The PubMed team annotates all incoming articles with their standardised and hierarchical search terms. You can find out about them by searching the MeSH database [http://www.ncbi.nlm.nih.gov/sites/entrez?term=cell&cmd=search&db=mesh]. After you have found appropriate terms use them for searching. Type, for example:		The NCBI provides you with standardised search vocabulary. This is advantageous because the right MeSH term (medical subject heading) will find all articles using various synonyms of the term. For example, a brute text search for ''translation'' will not return publications using the synonym ''protein synthesis''. The PubMed team annotates all incoming articles with their standardised and hierarchical search terms. You can find out about them by searching the MeSH database [http://www.ncbi.nlm.nih.gov/sites/entrez?term=cell&cmd=search&db=mesh]. After you have found appropriate terms use them for searching. Type, for example:

-	{\| border=1 cellpadding=5 cellspacing=0	+	{\| border=1 cellpadding=5 cellspacing=0
	\| ''protein biosynthesis'''[mh]''' stem cells'''[mh]'''''		\| ''protein biosynthesis'''[mh]''' stem cells'''[mh]'''''
	\| This returns all publications that have ''protein biosynthesis'' (translation) AND ''stem cells'' as MeSH terms. PubMed automatically assumes AND as boolean. You can specify OR if required, but connectors have to be capitalised otherwise they are not recognised!		\| This returns all publications that have ''protein biosynthesis'' (translation) AND ''stem cells'' as MeSH terms. PubMed automatically assumes AND as boolean. You can specify OR if required, but connectors have to be capitalised otherwise they are not recognised!
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	{\| border=1 cellpadding=5 cellspacing=0		{\| border=1 cellpadding=5 cellspacing=0
-	\|'''[au]'''	+	\|valign=top\|'''[au]'''
-	\|author name; e.g. ''"smith g"[au]''; without quotes~~, results~~ will include Smith GX with X being any initial or ~~empty~~	+	\|author name; e.g. ''"smith g"[au]''
		+	<div style="font-size:90%">
		+	*searching without quotes will include Smith GX, with X being any initial or none
		+	*abstain from punctuation - just confuses PubMed; also don't put the initial 1st; ''Smith, G'', ''Smith G.'', or ''G Smith'' won't work
		+	*''Smith G'' and author names in the same format are recognised as an author name even without the [au] tag
		+	</div>
	\|-		\|-
-	\|'''[ti]'''	+	\|valign=top\|'''[ti]'''
-	\|article title; e.g. ''stem cells[ti]'' - note that even without quotes ''stem cells'' is considered a phrase	+	\|article title; e.g. ''stem cells[ti]''
		+	<div style="font-size:90%">
		+	*note that even without quotes ''stem cells'' is considered a phrase
		+	</div>
	\|-		\|-
-	\|'''[ta]'''	+	\|valign=top\|'''[ta]'''
-	\|journal title; e.g. ''nature[ta]''; who ~~know~~ why this field name was chosen	+	\|journal title; e.g. ''nature[ta]''
		+	<div style="font-size:90%">
		+	* who knows why this field name was chosen; Title of journAl?
		+	</div>
	\|-		\|-
-	\|'''[dp]'''	+	\|valign=top\|'''[dp]'''
-	\|date of publication; e.g. ''2006[dp]'' or ''2006/01[dp]'' for January 2006; format is YYYY/MM/DD[dp]; month and day are optional~~<br>~~	+	\|date of publication; e.g. ''2006[dp]'' or ''2006/01[dp]'' for January 2006
-	can also be used in different ways: e.g. ''"last 10 days"[dp]'' or ''"last 2 months"[dp]'' (quotes are required)~~<br>~~	+	<div style="font-size:90%">
-	or ''1998:1999[dp]'' for all publications from '98 to '99	+	*format is YYYY/MM/DD[dp]; month and day are optional
		+	*can also be used in different ways: e.g. ''"last 10 days"[dp]'' or ''"last 2 months"[dp]'' (quotes are required)
		+	*or ''1998:1999[dp]'' for all publications from '98 to '99
		+	</div>
	\|}		\|}

Jakob Suckale: links

2007-06-04T18:06:39Z

links

←Older revision		Revision as of 18:06, 4 June 2007
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-	[[Image:Hardcore_pubmeding.png\|right]]	+	[[Image:Hardcore_pubmeding.png\|right\|hspace=20]]

	'''PubMed''' [http://en.wikipedia.org/wiki/PubMed] at http://www.pubmed.org is maybe the '''best search machine for articles in biology'''. It is run by the NCBI [http://www.ncbi.nlm.nih.gov/], USA, and gives you the possibility to search a gigantic archive of life science literature.		'''PubMed''' [http://en.wikipedia.org/wiki/PubMed] at http://www.pubmed.org is maybe the '''best search machine for articles in biology'''. It is run by the NCBI [http://www.ncbi.nlm.nih.gov/], USA, and gives you the possibility to search a gigantic archive of life science literature.
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	* PubMed in the wikipedia [http://en.wikipedia.org/wiki/PubMed]		* PubMed in the wikipedia [http://en.wikipedia.org/wiki/PubMed]
	* PubMed E-utilities [http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html]		* PubMed E-utilities [http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html]
		+	* NCBI help page on My NCBI customisation [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.My_NCBI]

Jakob Suckale: layout, corrections

2007-06-04T18:00:47Z

layout, corrections

←Older revision		Revision as of 18:00, 4 June 2007
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	{\| border=1 cellpadding=5 cellspacing=0		{\| border=1 cellpadding=5 cellspacing=0
-	\| ''protein biosynthesis[mh] stem cells[mh]''	+	\| ''protein biosynthesis'''[mh]''' stem cells'''[mh]'''''
	\| This returns all publications that have ''protein biosynthesis'' (translation) AND ''stem cells'' as MeSH terms. PubMed automatically assumes AND as boolean. You can specify OR if required, but connectors have to be capitalised otherwise they are not recognised!		\| This returns all publications that have ''protein biosynthesis'' (translation) AND ''stem cells'' as MeSH terms. PubMed automatically assumes AND as boolean. You can specify OR if required, but connectors have to be capitalised otherwise they are not recognised!
	\|-		\|-
-	\| ''protein biosynthesis[mj] stem cells[mj]''	+	\| ''protein biosynthesis'''[mj]''' stem cells'''[mj]'''''
	\| Replace the tag ''[mh]'' with ''[mj]'' to get back only publications that have the term in question as a ''major (mj) topic''. This will significantly reduce the search hits.		\| Replace the tag ''[mh]'' with ''[mj]'' to get back only publications that have the term in question as a ''major (mj) topic''. This will significantly reduce the search hits.
	\|}		\|}
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	{\| border=1 cellpadding=5 cellspacing=0		{\| border=1 cellpadding=5 cellspacing=0
-	\|[au]	+	\|'''[au]'''
	\|author name; e.g. ''"smith g"[au]''; without quotes, results will include Smith GX with X being any initial or empty		\|author name; e.g. ''"smith g"[au]''; without quotes, results will include Smith GX with X being any initial or empty
	\|-		\|-
-	\|[ti]	+	\|'''[ti]'''
	\|article title; e.g. ''stem cells[ti]'' - note that even without quotes ''stem cells'' is considered a phrase		\|article title; e.g. ''stem cells[ti]'' - note that even without quotes ''stem cells'' is considered a phrase
	\|-		\|-
-	\|[ta]	+	\|'''[ta]'''
	\|journal title; e.g. ''nature[ta]''; who know why this field name was chosen		\|journal title; e.g. ''nature[ta]''; who know why this field name was chosen
	\|-		\|-
-	\|[dp]	+	\|'''[dp]'''
	\|date of publication; e.g. ''2006[dp]'' or ''2006/01[dp]'' for January 2006; format is YYYY/MM/DD[dp]; month and day are optional<br>		\|date of publication; e.g. ''2006[dp]'' or ''2006/01[dp]'' for January 2006; format is YYYY/MM/DD[dp]; month and day are optional<br>
	can also be used in different ways: e.g. ''"last 10 days"[dp]'' or ''"last 2 months"[dp]'' (quotes are required)<br>		can also be used in different ways: e.g. ''"last 10 days"[dp]'' or ''"last 2 months"[dp]'' (quotes are required)<br>
-	or ''1998:1999[dp]'' for all publications ~~in these two years~~	+	or ''1998:1999[dp]'' for all publications from '98 to '99
	\|}		\|}

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	== My NCBI - personalising PubMed ==		== My NCBI - personalising PubMed ==

-	PubMed offers you the possibility to save your searches for reuse and automatic email alerts. You need to register for this option. My NCBI[http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.My_NCBI] also allows you to set up filters[http://www.nlm.nih.gov/bsd/viewlet/myncbi/filters.html], define document delivery options, and set user preferences. You will find the link on the left of PubMed main search page [http://www.ncbi.nlm.nih.gov/entrez/login.fcgi?call=0NTQw95KEIM-1pLA3kA7v3&callpath=07DWAO_5VfJ7C9hKuVcix_f5C5gyMoBc3h7s&db=pubmed.]	+	PubMed offers you the possibility to save your searches for reuse and automatic email alerts. You need to register for this option. My NCBI [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.My_NCBI] also allows you to set up filters [http://www.nlm.nih.gov/bsd/viewlet/myncbi/filters.html], define document delivery options, and set user preferences. You will find the link on the left of PubMed main search page [http://www.ncbi.nlm.nih.gov/entrez/login.fcgi?call=0NTQw95KEIM-1pLA3kA7v3&callpath=07DWAO_5VfJ7C9hKuVcix_f5C5gyMoBc3h7s&db=pubmed.]

	== ''Related Articles'' function ==		== ''Related Articles'' function ==

Jakob Suckale: links

2007-06-04T17:58:23Z

links

←Older revision		Revision as of 17:58, 4 June 2007
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	{\| border=1 cellpadding=5 cellspacing=0		{\| border=1 cellpadding=5 cellspacing=0
	\|[au]		\|[au]
-	\|author name; e.g. ''"smith g"[au]''	+	\|author name; e.g. ''"smith g"[au]''; without quotes, results will include Smith GX with X being any initial or empty
	\|-		\|-
	\|[ti]		\|[ti]
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	== My NCBI - personalising PubMed ==		== My NCBI - personalising PubMed ==

-	PubMed offers you the possibility to save your searches for reuse and automatic email alerts. You need to register for this option. My NCBI also allows you to set up filters, define document delivery options, and set user preferences. You will find the link on the left of PubMed main search page [http://www.ncbi.nlm.nih.gov/entrez/login.fcgi?call=0NTQw95KEIM-1pLA3kA7v3&callpath=07DWAO_5VfJ7C9hKuVcix_f5C5gyMoBc3h7s&db=pubmed.]	+	PubMed offers you the possibility to save your searches for reuse and automatic email alerts. You need to register for this option. My NCBI[http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.My_NCBI] also allows you to set up filters[http://www.nlm.nih.gov/bsd/viewlet/myncbi/filters.html], define document delivery options, and set user preferences. You will find the link on the left of PubMed main search page [http://www.ncbi.nlm.nih.gov/entrez/login.fcgi?call=0NTQw95KEIM-1pLA3kA7v3&callpath=07DWAO_5VfJ7C9hKuVcix_f5C5gyMoBc3h7s&db=pubmed.]

	== ''Related Articles'' function ==		== ''Related Articles'' function ==

Jakob Suckale: small corrections

2007-06-02T18:13:08Z

small corrections

←Older revision		Revision as of 18:13, 2 June 2007
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	== ''Related Articles'' function ==		== ''Related Articles'' function ==

-	PubMed includes a very useful function to suggest related ~~artices~~ to the one(s) you just retrieved by a search. The feature relates articles by comparing their words [http://www.ncbi.nlm.nih.gov/entrez/query/static/computation.html]. You will find them on the right of the abstract page. Often this will help you to find article not spotted by your search but of interest to you.	+	PubMed includes a very useful function to suggest related articles to the one(s) you just retrieved by a search. The feature relates articles by comparing their words [http://www.ncbi.nlm.nih.gov/entrez/query/static/computation.html]. You will find them on the right of the abstract page. Often this will help you to find article not spotted by your search but of interest to you.

	== Further reading ==		== Further reading ==